From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Tue Jun 28 2005 - 03:31:38 CDT
Hi,
I am currently running an NPT simulation of ethanol and water. I have ran
my simulation for approximately 2 ns now, and I have a question concerning
the DCD trajectory file, boundary conditions and Wrap.
I did not specify WrapAll or WrapWater in my configuation file, so these
should be turned off by default. I calculated the radial distribution
function between the centers of mass of all of my ethanol molecules from
the DCD file. At first I neglected to consider the wrapping (or lack of
since I didn't specify WrapAll, etc) of my molecules. However, after I
took this into account, but I do not see any change.
Also, when I observe my trajectories in VMD, I do not (or I do not think
I) observe anything crossing system boundaries. I am only considering 64
and 512 ethanol molecules, and my cubic box length is around 40 - 46
Angstroms.
Does NAMD automatically wrap molecules when writing DCD files despite
having WrapAll or WrapWater turned off? Or is there something I am not
considering in the barostat that is affecting the wrapping or periodic
boundary conditions? I am using a Langevin temperature and pressure
control with the following parameter:
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
Many thanks.
Joshua Moore
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:39:38 CST